What’s the best tool to annotate PDFs?

We all know the workflow: a collaborator sends a draft proposal or paper; we carefully read it; bleed all over it; and send it back. I admit that until last year, I used a Big Red Pen on hardcopy, which I then returned to the lead author by scanning with the xerox machine.

Recently I switched over to marking PDF files using the Annotate menu in OS X’s Preview app. It’s pretty good, if a bit clunky. But maybe there’s a better way?

So let me ask an innocent-sounding question: What’s the best tool to annotate PDFs, and why? Why do you use the tool you use?

As someone who has just spent several months immersed in the proofreading process with about 30 collaborators spread around the world, let me just say that annotating PDF files has made this kind of feedback extremely easy. Seductively so. The problem with the method is that it appears to be much harder to find typos on a computer screen than on a sheet of paper. Maybe your brain slows down more on a sheet of paper. Maybe there is less glare. Whatever it is, if you really want to find typos, print the document out, pour yourself a beer, and get that Big Red Pen ready to roll.

Agreed: printing a paper out magically increases my attentiveness. But for most articles I also use Annotate on Preview. The problems with moving comment boxes around and highlighting equations isn’t enough for me to make the effort to switch to something better (at least for now)!

I find the Note Tool function in the free Foxit Reader (http://www.foxitsoftware.com/pdf/reader/) very handy for marking up documents and sending back to colleagues, as the Notes can also be seen in other PDF viewers, including Adobe Reader and the evince Document Viewer.

For KDE users, Okular will allow you to annotate virtually any document with all sorts of highlighting, underlining, and sticky note-type tools. Unfortunately, I don’t think the annotations are viewable in other document readers. The annotations are saved locally, so to send the annotated version to someone else you must export it with “File > Export as > Document archive.”

I’ve been using (an old version of) Adobe Acrobat Pro, which I find extremely useful and quite easy to use. However it’s not cheap, and I only have it on a windows box while I’d prefer to have a free software that would work on all my machines regardless of the OS (Linux or Windows).

For Macs, I use Skim and Papers. Skim is really quite nice, does highlighting, annotations, free-form, etc. It also works pretty well with Papers and Dropbox, so I have my papers library synced across all my macs.

For iPad users (I read almost all papers on my iPad now), I highly recommend iAnnotate PDF. Supports the full range of PDF annotations – underline, strike, scribbles, etc. – and allows you to make typed-text notes associated with any of them.

When you’re done, you can email the annotated file from within the app, and it’s viewable in all standard PDF readers (Adobe, Preview, Foxit, etc.). There are cheaper (free, even) iPad apps, but they tend to rasterize the PDF instead of using the annotation layer.

Also includes Dropbox integration, so you can pull papers directly from your Dropbox, annotate, then one-tap upload them.

I have been using Preview’s annotate feature for getting / giving feedback on paper drafts with collaborators. I find these much more convenient than the Big Red Pen (no need to decipher what that curly character means), text emails detailing the comments like your journal referee (no need to find page 15, paragraph 3, sentence 4), or scanned hard copies.

One very useful feature: in the sidebar, you can switch to “Annotations” view and it will list all the comments. When I am done with the comment, I can delete (or minimize) it, giving me a measure of what I have accomplished. The notes can also be of different color, making the parsing process much easier when multiple commenters are involved. One feature that is lacking is being able to combine annotations from two different people (on the same file), but here I might be getting too greedy.

Adobe Reader, not just Adobe Acrobat Pro, has the Annotations features as well. While I find it to be less friendly (although my most recent version 10.0.2 looks better), it is cross-platform and allows you to share your PDFs with collaborators. Preview/Acrobat do a fairly good, but not perfect, job of reading annotations from each other.

Hopefully, this post pushes people to collectively start using annotated PDFs.

Only slightly off-topic – minimise the amount of PDF mark-up you have to do, and make the whole collaborative paper writing process faster and more efficient by treating latex like code and using versioning systems like cvs, svn or git. Then your co-authors can make their edits directly, and leave their comments in place – and successive revisions are stored (backed up offsite!) for later recall while you all only ever work on one file. Macros like this help for commenting:

One thing that’s hinted at, but not stated directly is that you gotta be careful about interoperability! I don’t know the details, but I know that Skim and Preview/Acrobat handle annotations very differently. Last I looked into this, the annotations made in Skim can’t be seen in Preview unless you specifically export them. And then they are not editable. Just looking at the above comments, it looks like Acrobat, Preview, and iAnnotate annotations play nice with each other.

Now, the advantage of Skim is that the annotations are basically stored as a text file that can be read by other programs. They beauty is that they show up in the Comments in BibDesk and are searchable! Which, as far as I know, is not true of annotations made with other programs.

So, when I’m making notes for myself in published journal articles (usually highlights or underlines), I use Skim + BibDesk. However, if I’m making comments on someone’s manuscript, I use Preview. (or eventually iAnnotate once I get my iPad.)

Can anyone comment on the nature of annotations in Papers 2?

Also, alt-click comes in super handy for highlighting and underlining in 2-column format.

OH! I’ve also had trouble printing with highlighting…If I recall, printing a PDF after I’ve highlighted in Acrobat results in solid blocks of color over the exact bits that I’m most interested in. The color is ON TOP of the text thus blocking it. This may be something that has been fixed…I encountered this problem several years ago.

I’ve had the same problems with printing from Acrobat, it seems to get very confused about the layering of things. I’ve had posters printed with the background put on top of everything else.

I’ve gotten around it by finding a little check box marked something like “Print as Image” in the advanced print options which has fixed the layering issues for me every time. It’s still annoying that the issue exists, though.

So I saw Matt’s comments about iAnnotate on the iPad. Does anyone know how it compares to Papers on iPad? There seem to be a lot more users(and reviews) for the former, but it’s probably due to the fact that the latter is more expensive. If anyone has any opinions on the two, I’d love to hear them. Thanks

I checked out Papers as well and eventually settled on iAnnotate. Main reason was that at the time Papers didn’t support annotations at all. Papers now does support some annotations, but they’re almost useless because they won’t sync to the desktop yet (I think you can email them though).

My full setup is a Dropbox folder for storage, iAnnotate for markup, and Mendeley on the desktop for its excellent bibtex support.

Does Mendeley automatically incorporate the markups made in iAnnotate? That is, if I open a paper in Mendeley that I have annotated in iAnnotate, will I see the markups? Or will I have to open the file externally with Adobe or Skim?

Also, I have heard some people say that Skim can do free hand annotation, but I haven’t seen the functionality.

I agree that Mendeley works nicely for annotations – tough not so good for old papers. There’s an option to exclude documents from your library, so if you’re just annotating a draft document or paper it won’t, e.g., get added to any .bib files you create from within Mendeley.

My comment is more along the line of Phil’s. If you have co-authors of the paper, why not add the corrections to the LaTeX source file itself? My collaborators and I use CVS to keep track of changes to our papers, and we use marginpar’s to annotate small features within a paper – more large-scale changes are usually highlighted with some color scheme, such as the one Phil mentioned.

@Phil and @Chris, Based on my personal experience, collaborators are more willing to read from and comment on PDFs rather on the TeX, unless there are major changes to be made. The formatting (and figures) makes it easier to read and comment.

I have tried a lot of annotation solutions and to be honest I find most of them fiddly and annoying, especially when the red pen+hard copy option is available. A.nnotate has the smoothest user experience of any I have tried. The existing notes stay out of the way when you are trying to read or add more notes. It is definitely much more usable than Acrobat, Preview, Skim or Mendeley IMO. It is web-based so it is automatically cross-platform.

whoohoo! i was hoping this tool would get mentioned. Maybe there will be some interest in going off thread to talk about sharing and reusing these annotations. Besides big red X or ? marks or while circles scrawled across the paper, one could actually imagine these as a form of micro-publication or in capturing (or enabling open) peer review and post-publication review or to add data links to papers…

I’ve used a couple of methods, most of which have been mentioned. I use Skim quite a bit for PDFs such as forms. To get those to come out right, I needed to “print to PDF” from within skim, to keep all the annotations. Preview annotations are great, but if you’re still using 10.5, then you can’t print the annotations from collaborators using 10.6 (or at least, I couldn’t).

For those still using the Big Red Pen method (which I agree is better for nit-picking and minor typos), most new photocopiers will scan to PDF, and email them straight to the first author as an attachment. Love that feature!

We’ve standardised on keeping everything in Dropbox folders, for collaborative edits. I like phil’s macros for commenting…will definitely have to borrow those!

I found a free website (http://www.pdfescape.com) that allows one to annotate any PDF document, the only restrictions: the PDF has to be less than 100 pages, and smaller than 10 MB (though you can always chop up larger documents).

The site offers several features, including: text boxes, collapsible sticky notes (which appear as comments when opened with Acrobat Reader), and the ability to draw simple shapes (e.g. lines, rectangles, and ellipses). If you create an account, you can leave the PDFs that you upload on their servers for two weeks, otherwise you need to download the changes before leaving the site.

I am currently using this site for my PhD thesis, and I like it not only because it saves my advisor the trip to a scanner/fax machine, but it saves me from having to decipher my advisor’s handwriting

Hi,
I use XOURNAL on Linux. You can go to the menu and select “Annotate pdf”,
in order to open pdf file, and you can do your annotations with your pen tablet or your tablet pc.
Xournal has good annotation features (different pens, colors, markers, figures, lines, triangles,
etc.). At the end, you can export to pdf and that’s all. And I think the size of final
file is increased only a little bit.
Regards

I have a related but different situation. I am a teacher that uses a PDF textbook and am trying to get the students to take notes that I can review. So, I do not want the original changed but want the students to be able to highlight, bubble, write notes, audio(?), etc. When they are done I would like to be able to get a version of the notes without getting multiple copies of the text chapter. This online system is the direction of the K-12 standardized testing is going and the students need too become familiar with analyzing readings online. Which application might be useful?

It can annotate PDFs, fill forms, edit content, OCR. There is no form designer but should be added soon (version 9). It is compliant with the Adobe PDF specifications / format which means that all annotations you add or form fields will also be visible by any other PDF viewer.

There is a really simple yet robust tool for extracting highlights and notes from your pdf-files available at: http://www.sumnotes.net . Not only it supports various advanced features like selective extraction or predictive extraction, but it also allows you to save extracted highlights into TXT or DOC files. And yes, it is for free. Try it out

I’ve tried marking up documents on my iPad, on my Windows tablet PC and on paper. I found I did not do as thorough a job using the iPad apps in editing. The mark-ups via the tablet seemed to work the best. Simple enough to do when the document came to me as a Word file. With a Word doc I used Microsoft Ink with the tablet. It worked better in my opinion then the iPad with a JotPro stylus–one of the finest points available for iPad use. While hard-copy paper worked as well as ever, Microsoft Ink with the stylus on my Windows tablet PC was the closest to paper.
To deal with the issue of how to mark-up a PDF on a Windows tablet, it was simplest to open the PDF in Adobe Acrobat–not Reader–that I had on another computer, save it as a Word doc and mark-up at will with the Microsoft Ink tools via Word.

I went looking for a tablet-and-pen solution, as I seem to require the capability to write in the margins, circle text freehand, cross out, draw little pictures etc.
Of the few packages I tried, including iAnnotate, NoteTaker HD (http://www.notetakerhd.com) on the iPad provides an experience most similar to the traditional paper & red pen. Primarily it’s for taking freehand notes, but also allows importing PDFs; it sets each page of the PDF as a “background” to a document, and then you are free to write all over it.
Transferring the annotated PDFs is a bit of a pain, as is (seemingly) getting anything on or off an iPad, but you can email the annotated document to yourself (or directly to whomever is asking for comments). Many other useful features.
I found the other aspects of the iPad too tiresome for words, so am now looking at alternative hardware, perhaps a Samsung Galaxy Note. Unfortunately NoteTaker HD is not available for Android yet.